--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Nov 03 18:54:22 WET 2017
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
tcoffee.params=
tcoffee.maxSeqs=0
codeml.bin=codeml
mrbayes.tburnin=2500
codeml.dir=
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb_adops
tcoffee.bin=t_coffee_ADOPS
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/revmuscle/S1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
(Use the harmonic mean for Bayes factor comparisons of models)
(Values are saved to the file /opt/ADOPS1/revmuscle/S1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -8407.61 -8434.37
2 -8408.23 -8427.50
--------------------------------------
TOTAL -8407.88 -8433.67
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/revmuscle/S1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
Summaries are based on a total of 3002 samples from 2 runs.
Each run produced 2001 samples of which 1501 samples were included.
Parameter summaries saved to file "/opt/ADOPS1/revmuscle/S1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.615000 0.003855 1.489043 1.728868 1.614820 1293.94 1363.25 1.000
r(A<->C){all} 0.113795 0.000123 0.092833 0.136175 0.113340 877.82 878.72 1.000
r(A<->G){all} 0.297668 0.000307 0.264210 0.333234 0.297581 845.46 944.45 1.000
r(A<->T){all} 0.073101 0.000048 0.059977 0.086706 0.072979 1030.75 1124.89 1.000
r(C<->G){all} 0.151349 0.000204 0.122423 0.177557 0.150920 809.21 892.97 1.000
r(C<->T){all} 0.268947 0.000281 0.236595 0.302259 0.268763 744.55 830.00 1.000
r(G<->T){all} 0.095139 0.000082 0.076825 0.112023 0.094966 990.39 1059.26 1.000
pi(A){all} 0.294934 0.000117 0.273250 0.316270 0.295037 882.72 903.80 1.001
pi(C){all} 0.171998 0.000074 0.154930 0.188431 0.172105 919.52 928.33 1.001
pi(G){all} 0.188299 0.000081 0.171177 0.205876 0.188070 1082.71 1139.64 1.000
pi(T){all} 0.344769 0.000124 0.323190 0.366707 0.344840 1009.41 1051.09 1.001
alpha{1,2} 0.859955 0.011700 0.663738 1.066380 0.848215 1179.72 1340.36 1.000
alpha{3} 1.962182 0.176401 1.276827 2.781067 1.909426 1373.25 1437.13 1.002
pinvar{all} 0.028637 0.000550 0.000001 0.075642 0.022985 786.56 915.25 1.000
------------------------------------------------------------------------------------------------------
* Convergence diagnostic (ESS = Estimated Sample Size); min and avg values
correspond to minimal and average ESS among runs.
ESS value below 100 may indicate that the parameter is undersampled.
+ Convergence diagnostic (PSRF = Potential Scale Reduction Factor; Gelman
and Rubin, 1992) should approach 1.0 as runs converge.
Setting sumt conformat to Simple
--- CODEML SUMMARY
Model 1: NearlyNeutral -6277.477622
Model 2: PositiveSelection -6240.076616
Model 0: one-ratio -6406.519925
Model 3: discrete -6237.962176
Model 7: beta -6284.142099
Model 8: beta&w>1 -6237.350098
Model 0 vs 1 258.08460599999853
Model 2 vs 1 74.8020120000001
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S1_SFBB1)
Pr(w>1) post mean +- SE for w
40 N 1.000** 3.457
46 R 1.000** 3.456
50 P 0.997** 3.451
79 L 0.998** 3.452
84 F 0.884 3.171
86 E 0.987* 3.426
88 G 0.799 2.963
98 L 0.581 2.427
99 A 0.913 3.243
126 R 0.834 3.049
134 I 0.971* 3.386
136 T 0.999** 3.454
153 Q 0.914 3.245
164 E 0.546 2.341
197 E 0.641 2.576
216 T 0.997** 3.450
218 E 0.953* 3.341
246 K 0.947 3.327
Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S1_SFBB1)
Pr(w>1) post mean +- SE for w
40 N 1.000** 3.541 +- 0.242
46 R 1.000** 3.541 +- 0.245
50 P 0.997** 3.534 +- 0.276
79 L 0.998** 3.536 +- 0.269
84 F 0.868 3.198 +- 0.885
86 E 0.987* 3.507 +- 0.378
88 G 0.776 2.962 +- 1.073
98 L 0.547 2.375 +- 1.261
99 A 0.902 3.289 +- 0.785
126 R 0.813 3.058 +- 1.007
134 I 0.969* 3.461 +- 0.501
136 T 0.999** 3.538 +- 0.256
153 Q 0.908 3.306 +- 0.770
164 E 0.510 2.281 +- 1.264
197 E 0.605 2.523 +- 1.239
216 T 0.997** 3.534 +- 0.277
218 E 0.948 3.408 +- 0.610
246 K 0.941 3.388 +- 0.642
Model 8 vs 7 93.5840019999996
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S1_SFBB1)
Pr(w>1) post mean +- SE for w
2 R 0.606 2.133
23 M 0.531 1.976
40 N 1.000** 2.984
46 R 1.000** 2.984
50 P 0.999** 2.982
79 L 0.999** 2.982
84 F 0.957* 2.895
86 E 0.994** 2.971
88 G 0.917 2.810
98 L 0.793 2.546
99 A 0.967* 2.915
111 G 0.559 2.029
126 R 0.932 2.840
134 I 0.988* 2.959
136 T 1.000** 2.983
153 Q 0.958* 2.896
164 E 0.774 2.505
168 Y 0.615 2.170
182 T 0.535 1.980
197 E 0.842 2.651
200 C 0.684 2.311
216 T 0.999** 2.982
218 E 0.981* 2.943
246 K 0.980* 2.942
269 T 0.683 2.311
Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S1_SFBB1)
Pr(w>1) post mean +- SE for w
2 R 0.617 2.008 +- 0.997
23 M 0.562 1.879 +- 0.972
40 N 1.000** 2.914 +- 0.500
46 R 1.000** 2.914 +- 0.500
50 P 0.999** 2.911 +- 0.505
79 L 0.999** 2.912 +- 0.504
84 F 0.943 2.774 +- 0.666
86 E 0.993** 2.899 +- 0.525
88 G 0.896 2.661 +- 0.762
98 L 0.766 2.344 +- 0.911
99 A 0.958* 2.814 +- 0.630
111 G 0.579 1.917 +- 0.992
126 R 0.913 2.701 +- 0.733
134 I 0.987* 2.883 +- 0.548
136 T 0.999** 2.913 +- 0.502
153 Q 0.954* 2.807 +- 0.646
164 E 0.746 2.295 +- 0.922
165 Q 0.520 1.793 +- 0.995
168 Y 0.625 2.008 +- 0.935
182 T 0.563 1.882 +- 0.985
197 E 0.806 2.439 +- 0.873
200 C 0.676 2.133 +- 0.956
216 T 0.999** 2.911 +- 0.505
218 E 0.977* 2.860 +- 0.578
246 K 0.975* 2.853 +- 0.584
269 T 0.668 2.107 +- 0.942
